The intelligence agencies are not under "the presidents control". They are authorized and funded by congress. They exist to provide intelligence to various congressional committees like the senate intelligence committee.
All of the government is funded by congress. But that doesn't change the fact that the defense agencies, the civil service, the intelligence agencies, etc. are all executive branch departments and are under the control of the president.
The way the government and civil service are supposed to work is that the country expresses its wishes via elections and the representatives elected set the policy and create laws. The civil service's purposes is to enact those policies and laws. What they don't get to do is set their own policy or create their own laws (yes, they do get to create some regulations but only within the scope outlined by congress.)
